ampliconduo
function, a list of ampliconduo data frames. Generates for each ampliconduo data frame a plot with freqB
over freqA
and arranges them in a 2-dimensional array, whereas plots in the same row and column share the same scale. Points with a p-value or adjusted p-value below a certain treshold are colored differently (default: red) indicating significant deviations of amplicon occurences between the two samples in an ampliconduo data frame.
plotAmpliconduo.set(x, color.treshold = 0.05, xlab = "Abundance (PCR A)",
ylab = "Abundance (PCR B)",log = "xy", corrected = TRUE, asp = 1, nrow = 1,
legend.position = NULL, save = FALSE, path = NULL, file.name = NULL,
format = "jpeg", h.start = 0, ...)
ampliconduo
function.
FALSE
), or corrected p-value (TRUE
) is used for coloring.
Default value is TRUE
.
FALSE
.
save
was set to TRUE
, specifies the directory (no backslash or slash at the end) for saving.
By default (parameter save
is set to TRUE) the plot is saved in the working directory.
save
was set to TRUE
specifies the file name for the plot.
The default name is ampliconduo_ampliconduo
function, that nicely visualizes those amplicons with a significant deviations in read numbers between the two amplicon data sets. The data in x
are transformed and passed to the qplot
function. The 2-dimensional arrangement of the different plots is achieved using facet_wrap
. Important aestetic parameters like color, aspect ratio, legend position ... are easily customized. Optionally, the plot can be saved in a variety of formats.
qplot
, used by plotAmpliconduo.set
to create the plots.
facet_wrap
, called for 2-dimensional arrangement of the plots.
plotAmpliconduo
, generates a very similar plot for a single ampliconduo data frame.
ampliconduo
, generates the input data, an ampliconduo data frame.
## loads example data of ampliconduo data frames
data(amplicons)
## plot amplicon frequencies of multiple ampliconduo data frames
plotAmpliconduo.set(amplicons[1:4], nrow = 3, h.start = 100)
plotAmpliconduo.set(amplicons[1:4], nrow = 1, corrected = FALSE, color.treshold = 0.1)
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